BRIG genome visualization missing rings - Solved!

Problem: 

Missing rings for the query sequences and BRIG doesn't give any error message.

Solution that worked for me:

This is an issue with java version. I was running Java 1.8 version and had same problem as the OP's question. Then I followed the answers and finally changing the java version worked for me.

I ran the following steps

1) Go to link: https://www.oracle.com/java/technologies/javase-java-archive-javase6-downloads.html 

2) mkdir Java1.6

3) Download "jdk-6u45-linux-x64.bin" and save in Java1.6

3) cd Java1.6 && chmod +x jdk-6u45-linux-x64.bin

4) You should see java file in Java1.6/jdk1.6.0_45/bin

5) Java1.6/jdk1.6.0_45/bin/java -version - should give "1.6.0_45"

6) Open BRIG using Java1.6 as follows:

Java1.6/jdk1.6.0_45/bin/java -jar BRIG.jar

Note: I did not uninstall my original Java1.8 rather used the downloded java1.6 execulatable file using path. That way I retain both versions without any problem.

This gave me all the rings without any issue!! Hope this helps someone!

https://www.researchgate.net/post/Why_does_BRIG_fail_to_create_rings_for_some_of_the_genomes

Posted my answer in research gate - click above link to see the discussion

SRST2 requires a specific naming convention for input fastq files

 SRST2 Trouble installing in server

 Also wanted to mention that SRST2 has been there for a while now (last updated was 2015) and I had some issues with running server because of dependency issues of bowtie2 tool (libstd, libtbb). 

 

SRST2 Trouble with specific versions of bowtie

 

Also, SRST2 only needs a specific version of bowtie2 (between 2.10 to 2.2.9 - but the latest is 2.4.1) causing some problem to work on server. 

 

SRST2 installation

 

Finally installed SRST2 on using conda. https://anaconda.org/bioconda/srst2

 

SRST2 requires a specific naming convention

 

An other issue with SRST2 is the naming, since it accepts the names like _S1_L001_R1_001.fastq.gz. 

For those samples which does not have a convention " _S1_L001_R1_001.fastq", created a symlink dummy with " _S1_L001_R1_001.fastq". 

For example, "filename_L001_R1_001.fastq" does not follow the SRST2 input convention, so created a symlink file filename_S1_L001_R1_001.fastq.